Best Small Business Bookkeeping Software with Payroll in 2025
Managing finances is a critical task for small business owners, and choosing the right bookkeeping software with integrated payroll functionality can streamline operations, ensure compliance, and save valuable time. This article explores the top bookkeeping software options for small businesses in 2025 that include payroll features, optimized for ease of use, affordability, and scalability. Whether you’re a freelancer, sole proprietor, or managing a growing team, these tools can simplify your financial management.
Why Small Businesses Need Bookkeeping Software with Payroll
Bookkeeping software with payroll integration automates essential tasks such as tracking income, expenses, and employee payments, reducing manual errors and ensuring compliance with tax regulations. These tools provide real-time financial insights, generate professional invoices, and streamline payroll processes, including tax filings and direct deposits. For small businesses, especially those with limited accounting expertise, such software is invaluable for maintaining accurate records and improving cash flow management.
Key Features to Look for in Bookkeeping Software with Payroll
When selecting bookkeeping software with payroll, small business owners should prioritize the following features:

Double-Entry Accounting: Ensures accurate financial records by recording each transaction twice (debit and credit).
Payroll Automation: Manages employee payments, tax calculations, and filings seamlessly.
Integration with Bank Accounts: Automatically imports and categorizes transactions for efficient reconciliation.
Invoicing and Payment Processing: Simplifies billing and allows clients to pay online via credit cards, PayPal, or bank transfers.
Tax Compliance: Supports tax calculations and filings, including compliance with regulations like Making Tax Digital (MTD) in the UK or IRS requirements in the US.
Scalability: Offers plans that grow with your business, accommodating additional users or features as needed.
User-Friendly Interface: Intuitive design for business owners with minimal accounting knowledge.
Reporting and Analytics: Provides detailed financial reports for informed decision-making.

Top Bookkeeping Software with Payroll for Small Businesses in 2025
Below is a curated list of the best bookkeeping software options that include payroll functionality, based on usability, features, and affordability.
1. QuickBooks Online
Best for Comprehensive Features and Scalability
QuickBooks Online is a leading choice for small businesses due to its robust feature set and user-friendly interface. It supports double-entry accounting, invoicing, expense tracking, and payroll management. The payroll add-on automates tax calculations, direct deposits, and filings, making it ideal for businesses with employees. QuickBooks integrates with over 300 third-party apps, including PayPal and Shopify, enhancing its flexibility. While it’s on the pricier side, its scalability makes it suitable for businesses with growing needs.

Key Features: AI-powered reconciliation, payroll with tax filings, customizable reports, mobile app.
Pricing: Starts at $30/month (plus payroll add-on, approximately $45/month + $6/employee).
Best For: Small businesses with a budget for advanced features and multiple employees.

2. Xero
Best for Integration and Multi-User Access
Xero is a cloud accounting software-based accounting solution that excels in providing payroll, invoicing, and expense tracking. Its payroll feature, available in select regions, integrates with platforms like Gusto for comprehensive tax and compliance support. Xero’s strength lies in its seamless integration with over 1,000 apps and its ability to support multiple users, making it ideal for collaborative teams. The software’s intuitive interface and real-time financial insights are perfect for micro-businesses and growing firms.

Key Features: Payroll integration with Gusto, bank reconciliation, extensive app integrations, project tracking.
Pricing: Starts at $15/month (payroll add-on varies by region, e.g., $10/month with Gusto).
Best For: Businesses needing third-party integrations and team collaboration.

3. FreshBooks
Best for Service-Based Businesses
FreshBooks is designed for freelancers and service-based businesses, offering an intuitive platform for bookkeeping and payroll. Its payroll feature, powered by Gusto, automates employee payments, tax filings, and benefits management. FreshBooks excels in invoicing, with automated reminders and online payment options to improve cash flow. While it supports basic inventory tracking, it’s best suited for businesses prioritizing simplicity and client management.

Key Features: Automated invoicing, payroll via Gusto, time tracking, expense categorization.
Pricing: Starts at $21/month (payroll add-on starts at $40/month + $6/employee).
Best For: Freelancers and service-based businesses with straightforward payroll needs.

4. Wave
Best for Budget-Conscious Businesses
Wave offers a free accounting and invoicing platform, with payroll as a paid add-on, making it an affordable option for sole proprietors and small businesses. The software supports double-entry accounting, bank reconciliation, and online payment processing. Its payroll feature handles employee payments and tax filings, though it’s limited to specific US states. Wave’s user-friendly interface and mobile app make it accessible for business owners with minimal accounting experience.

Key Features: Free accounting and invoicing, payroll with tax filings, receipt scanning, mobile app.
Pricing: Accounting is free; payroll starts at $20/month + $6/employee (US only).
Best For: Freelancers and small businesses with limited budgets.

5. Zoho Books
Best for Businesses Using Zoho Ecosystem
Zoho Books is a versatile accounting solution that integrates seamlessly with other Zoho applications, such as CRM and email. It offers payroll functionality in select regions, automating employee payments and tax compliance. Zoho Books supports double-entry accounting, inventory management, and customizable invoicing, making it suitable for growing businesses. Its free plan is ideal for small firms with annual revenue under $50,000.

Key Features: Payroll automation, integration with Zoho apps, inventory tracking, free plan for small firms.
Pricing: Free for businesses with < $50,000 revenue; paid plans start at $10/month (payroll add-on varies).
Best For: Businesses already using Zoho’s ecosystem or needing a free starter plan.

6. FreeAgent
Best for UK-Based Businesses
FreeAgent is tailored for UK freelancers and small businesses, offering MTD-compliant VAT filing, payroll, and invoicing. Its payroll feature automates payslips, pension contributions, and HMRC submissions, ensuring compliance. FreeAgent’s dashboard provides real-time cash flow insights, and its mobile app supports on-the-go expense tracking. It’s particularly appealing for businesses banking with NatWest or Royal Bank of Scotland, as they may qualify for free access.

Key Features: MTD compliance, payroll with HMRC integration, automated invoicing, cash flow tracking.
Pricing: Starts at $12/month (free for eligible UK bank customers).
Best For: UK-based freelancers and small businesses needing MTD compliance.

How to Choose the Right Bookkeeping Software with Payroll
Selecting the best software depends on your business’s size, industry, and budget. Consider the following:

Business Size: Sole proprietors and freelancers may prefer Wave or Zoho Books for affordability, while growing businesses benefit from QuickBooks or Xero’s scalability.
Industry Needs: Service-based businesses can opt for FreshBooks, while retail or inventory-heavy businesses may prefer Xero or Zoho Books.
Payroll Requirements: Ensure the payroll feature is available in your region (e.g., Wave’s payroll is US-only, FreeAgent is UK-focused).
Budget: Free or low-cost options like Wave and Zoho Books suit startups, while QuickBooks and Xero are worth the investment for advanced features.
Ease of Use: Look for intuitive interfaces and tutorials, especially if you lack accounting expertise.

Benefits of Using Bookkeeping Software with Payroll

Time Savings: Automates repetitive tasks like data entry, payroll processing, and tax calculations.
Accuracy: Reduces errors with double-entry accounting and automated reconciliations.
Compliance: